ClinVar Miner

Submissions for variant NM_024312.5(GNPTAB):c.204-15G>T (rs10860787)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000587904 SCV000975317 benign not provided 2018-06-19 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Illumina Clinical Services Laboratory,Illumina RCV000328472 SCV000375449 benign I cell disease 2016-06-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000380692 SCV000375450 benign Mucolipidosis, Type III Alpha/Beta 2016-06-14 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000587904 SCV000699477 benign not provided 2016-10-10 criteria provided, single submitter clinical testing Variant summary: The GNPTAB c.204-15G>T variant involves the alteration of a non-conserved intronic nucleotide. Mutation taster predicts a benign outcome for this variant along with 5/5 splice prediction tools predict no significant impact on splicing. This variant was found in 5864/121394 control chromosomes (675 homozygotes), predominantly observed in the East Asian subpopulation at a frequency of 0.3188339 (2756/8644). This frequency greatly exceeds the estimated maximal expected allele frequency of a pathogenic GNPTAB variant (0.0022361), indicating this is a benign polymorphism found primarily in the populations of East Asian origin. The variant of interest has not, to our knowledge, been reported in affected individuals via publications nor evaluated for functional impact by in vivo/vitro studies. One reputable clinical lab has classified the variant as benign. Taken together, this variant is classified as benign.
Mayo Clinic Genetic Testing Laboratories,Mayo Clinic RCV000587904 SCV000800959 benign not provided 2017-12-06 no assertion criteria provided clinical testing

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